chr3-20040862-T-G
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_003884.5(KAT2B):c.303+82T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0425 in 1,385,482 control chromosomes in the GnomAD database, including 1,960 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.071 ( 592 hom., cov: 31)
Exomes 𝑓: 0.039 ( 1368 hom. )
Consequence
KAT2B
NM_003884.5 intron
NM_003884.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.177
Genes affected
KAT2B (HGNC:8638): (lysine acetyltransferase 2B) CBP and p300 are large nuclear proteins that bind to many sequence-specific factors involved in cell growth and/or differentiation, including c-jun and the adenoviral oncoprotein E1A. The protein encoded by this gene associates with p300/CBP. It has in vitro and in vivo binding activity with CBP and p300, and competes with E1A for binding sites in p300/CBP. It has histone acetyl transferase activity with core histones and nucleosome core particles, indicating that this protein plays a direct role in transcriptional regulation. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP6
Variant 3-20040862-T-G is Benign according to our data. Variant chr3-20040862-T-G is described in ClinVar as [Benign]. Clinvar id is 1226690.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KAT2B | NM_003884.5 | c.303+82T>G | intron_variant | ENST00000263754.5 | |||
KAT2B | XM_005265528.5 | c.303+82T>G | intron_variant | ||||
KAT2B | XM_047449147.1 | c.-193+82T>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KAT2B | ENST00000263754.5 | c.303+82T>G | intron_variant | 1 | NM_003884.5 | P1 | |||
KAT2B | ENST00000426228.1 | n.83+82T>G | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.0713 AC: 10542AN: 147808Hom.: 588 Cov.: 31
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GnomAD4 exome AF: 0.0390 AC: 48322AN: 1237548Hom.: 1368 AF XY: 0.0400 AC XY: 24395AN XY: 609372
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GnomAD4 genome AF: 0.0714 AC: 10564AN: 147934Hom.: 592 Cov.: 31 AF XY: 0.0700 AC XY: 5061AN XY: 72254
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 12, 2021 | - - |
Computational scores
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Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at